diff --git a/tools/checkformat/.shed.yml b/tools/checkformat/.shed.yml
new file mode 100644
index 000000000..ff863e5d7
--- /dev/null
+++ b/tools/checkformat/.shed.yml
@@ -0,0 +1,8 @@
+name: checkformat
+owner: ethevenot
+description: '[W4M][Metabolomics][LC-MS][GC-MS][NMR] Checks the formats of the dataMatrix, sampleMetadata, and variableMetadata files.'
+homepage_url: http://workflow4metabolomics.org
+long_description: 'For all post-processing steps of the peak table, W4M uses a 3 table format for the data and metadata. This module therefore checks that the formats of the 3 files "dataMatrix.tsv", "sampleMetadata.tsv", and "variableMetadata.tsv" are correct. It can be used before any post-processing step (such as normalization or statistical analysis). Potential warnings or errors in the formats are returned in the "information.txt" output file.'
+remote_repository_url: https://github.com/workflow4metabolomics/checkformat.git
+categories:
+- Metabolomics
\ No newline at end of file
diff --git a/tools/checkformat/CHANGELOG.md b/tools/checkformat/CHANGELOG.md
new file mode 100644
index 000000000..c734b3cc3
--- /dev/null
+++ b/tools/checkformat/CHANGELOG.md
@@ -0,0 +1,25 @@
+# Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
+
+## [3.0.0+galaxy0] - 2025-07-16
+### Changed
+- migrated from Gitlab to GitHub
+
+## [3.0.0] - 2018-03-01
+### Added
+- Automated re-ordering (if necessary) of sample and/or variable names from `dataMatrix` based on `sampleMetadata` and `variableMetadata`.
+- New argument to make sample and variable names syntactically valid.
+- Output of `dataMatrix`, `sampleMetadata`, and `variableMetadata` files, whether they have been modified or not.
+
+## [2.0.4] - 2017-06-06
+### Changed
+- Minor internal modifications.
+
+## [2.0.2] - 2016-07-30
+### Changed
+- Test for R code.
+- Planemo running validation.
+- Planemo installing validation.
+- Travis automated testing.
\ No newline at end of file
diff --git a/tools/checkformat/checkformat_config.xml b/tools/checkformat/checkformat_config.xml
new file mode 100644
index 000000000..fcb4bbda4
--- /dev/null
+++ b/tools/checkformat/checkformat_config.xml
@@ -0,0 +1,177 @@
+<tool id="checkFormat" name="Check Format" version="3.0.0+galaxy0" license="CECILL-2.1" profile="23.0">
+  <description>Checking/formatting the sample and variable names of the dataMatrix, sampleMetadata, and variableMetadata files</description>
+  
+  <requirements>
+    <requirement type="package" version="4.3.3">r-base</requirement>
+  </requirements>
+
+  <required_files>
+    <include path="checkformat_script.R" />
+  </required_files>
+
+  <command detect_errors="aggressive"><![CDATA[
+    Rscript -e 'source("$__tool_directory__/checkformat_script.R")' -e "source('$run_script')"
+  ]]></command>
+
+  <configfiles>
+    <configfile name="run_script"><![CDATA[
+sink("$information", append=TRUE, split=TRUE)
+
+resLs <- readAndCheckF(
+  '$dataMatrix_in',
+  '$sampleMetadata_in',
+  '$variableMetadata_in',
+  $makeNameL
+)
+
+write_dataMatrix(resLs[["datMN"]], "$dataMatrix_out")
+write_metadata(resLs[["samDF"]], "$sampleMetadata_out")
+write_metadata(resLs[["varDF"]], "$variableMetadata_out")
+
+if (resLs[["chkL"]]) {
+  if (resLs[["newL"]]) {
+    cat("\nWarning: The sample and/or variable names or orders from the input tables have been modified\n(see the information file for details); please use the new output tables for your analyses.\n")
+  } else {
+    cat("\nThe input tables have a correct format and can be used for your analyses.\n")
+  }
+}
+    ]]></configfile>
+  </configfiles>
+  
+  <inputs>
+    <param name="dataMatrix_in" type="data" label="Data matrix file" format="tabular"
+      help="Tabular file containing the numeric data matrix (variables as rows, samples as columns). Row and column names must match those in the sample and variable metadata files. Use '.' as decimal and 'NA' for missing values. No extra metadata should be present." />
+    <param name="sampleMetadata_in" type="data" label="Sample metadata file" format="tabular"
+      help="Tabular file with sample metadata (samples as rows, metadata fields as columns). Row names must match the column names of the data matrix. Use '.' as decimal and 'NA' for missing values." />
+    <param name="variableMetadata_in" type="data" label="Variable metadata file" format="tabular"
+      help="Tabular file with variable metadata (variables as rows, metadata fields as columns). Row names must match the row names of the data matrix. Use '.' as decimal and 'NA' for missing values." />
+    <param name="makeNameL" label="Make syntactically valid sample and variable names" type="select"
+      help="If set to 'yes', sample and variable names will be converted to syntactically valid R names using the 'make.names' function (e.g., names starting with a digit will be prefixed with 'X', spaces will be replaced by '.', etc.).">
+      <option value="TRUE">yes</option>
+      <option value="FALSE" selected="true">no</option>
+    </param>
+  </inputs>
+  
+  <outputs>
+    <data name="dataMatrix_out" label="${tool.name}_${dataMatrix_in.name}" format="tabular"/>
+    <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular"/>
+    <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular"/>
+    <data name="information" label="${tool.name}_information.txt" format="txt"/>
+  </outputs>
+  
+  <tests>
+    <test>
+      <param name="dataMatrix_in" value="input-dataMatrix.tsv"/>
+      <param name="sampleMetadata_in" value="input-sampleMetadata.tsv"/>
+      <param name="variableMetadata_in" value="input-variableMetadata.tsv"/>
+      <param name="makeNameL" value="TRUE"/>
+      <output name="information">
+        <assert_contents>
+          <has_text text="Message: Converting sample and variable names to the standard R format" />
+          <has_text text="Warning: The sample and/or variable names or orders from the input tables have been modified" />
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
+  
+  <help><![CDATA[
+    
+.. class:: infomark
+    
+**Author** Etienne Thevenot (W4M Core Development Team, MetaboHUB Paris, CEA)
+    
+---------------------------------------------------
+   
+============
+Check Format
+============
+    
+-----------
+Description
+-----------
+    
+| **Checks the format (row and column names)** of the dataMatrix, sampleMetadata and variableMetadata tables; in case of difference of orders of the samples and/or variables between (some of) the tables, the **orders from the dataMatrix are permuted** to match those of the sampleMetadata and/or the variableMetadata; sample and variables names can also be modified to be **syntactically valid** for R by selecting the corresponding argument (e.g. an 'X' is added to names starting with a digit, blanks will be converted to '.', etc.).
+    
+    
+-----------------
+Workflow position
+-----------------
+    
+.. image:: ./static/images/checkFormat_workflowPositionImage.png
+
+    
+-----------
+Input files
+-----------
+ 
++----------------------------+---------+
+| Parameter : num + label    |  Format |
++============================+=========+
+| 1 : Data matrix file       | tabular |
++----------------------------+---------+
+| 2 : Sample metadata file   | tabular |
++----------------------------+---------+
+| 3 : Variable metadata file | tabular |
++----------------------------+---------+
+
+| The **required formats** for the dataMatrix, sampleMetadata, and variableMetadata files are described in the **HowTo** entitled 'Format Data For Postprocessing' available on the main page of Workflow4Metabolomics.org (https://nextcloud.inrae.fr/s/qLkNZRf84QQ5YLY).
+
+
+----------
+Parameters
+----------
+    
+Data matrix file
+  | variable x sample **dataMatrix** tabular separated file of the numeric data matrix, with . as decimal, and NA for missing values; the table must not contain metadata apart from row and column names; the row and column names must be identical to the rownames of the sample and variable metadata, respectively (see below)
+  |
+
+Sample metadata file
+  | sample x metadata **sampleMetadata** tabular separated file of the numeric and/or character sample metadata, with . as decimal and NA for missing values
+  |
+  
+Variable metadata file
+  | variable x metadata **variableMetadata** tabular separated file of the numeric and/or character variable metadata, with . as decimal and NA for missing values
+  |
+
+Make syntactically valid sample and variable names
+  | if set to 'yes', sample and variable names will converted to syntactically valid names with the 'make.names' R function when required (e.g. an 'X' is added to names starting with a digit, blanks will be converted to '.', etc.)
+  |
+  
+------------
+Output files
+------------
+
+dataMatrix_out.tabular
+  | dataMatrix data file; may be identical to the input dataMatrix in case no renaming of sample/variable names nor re-ordering of samples/variables (see the 'information' file for the presence/absence of modifications)
+  |
+
+sampleMetadata_out.tabular
+  | sampleMetadata data file; may be identical to the input sampleMetadata in case no renaming of sample names nor re-ordering of samples (see the 'information' file for the presence/absence of modifications)
+  |
+
+variableMetadata_out.tabular
+  | variableMetadata data file; may be identical to the input variableMetadata in case no renaming of variable names nor re-ordering of variables (see the 'information' file for the presence/absence of modifications)
+  |
+
+information.txt
+  | Text file with all messages when error(s) in formats are detected
+  |
+    
+---------------------------------------------------
+    
+---------------
+Working example
+---------------
+    
+.. class:: infomark
+  
+See the **W4M00001a_sacurine-subset-statistics**, **W4M00001b_sacurine-complete**, **W4M00002_mtbls2**, or **W4M00003_diaplasma** shared histories in the **Shared Data/Published Histories** menu.
+    
+  ]]></help>
+  
+  <citations>
+    <citation type="doi">10.1021/acs.jproteome.5b00354</citation>
+    <citation type="doi">10.1016/j.biocel.2017.07.002</citation>
+    <citation type="doi">10.1093/bioinformatics/btu813</citation>
+  </citations>
+</tool>
diff --git a/tools/checkformat/checkformat_script.R b/tools/checkformat/checkformat_script.R
new file mode 100644
index 000000000..c36cbe3c5
--- /dev/null
+++ b/tools/checkformat/checkformat_script.R
@@ -0,0 +1,218 @@
+## Etienne Thevenot
+## CEA, MetaboHUB Paris
+## etienne.thevenot@cea.fr
+
+
+
+## Reads the dataMatrix, sampleMetadata, and variableMetadata .tsv files
+## and checks the formats
+readAndCheckF <- function(datFilC = "dataMatrix.tsv",
+                          samFilC = "sampleMetadata.tsv",
+                          varFilC = "variableMetadata.tsv",
+                          makNamL) {
+    ## options
+
+    optStrAsFacL <- options()[["stringsAsFactors"]]
+    options(stringsAsFactors = FALSE)
+
+
+    ## checking that the tables have no duplicated row or column names
+
+    for (tabC in c("dat", "sam", "var")) {
+        tabNamC <- switch(tabC,
+            dat = "dataMatrix",
+            sam = "sampleMetadata",
+            var = "variableMetadata"
+        )
+
+        rowVc <- read.table(eval(parse(text = paste0(tabC, "FilC"))),
+            check.names = FALSE,
+            header = TRUE,
+            sep = "\t"
+        )[, 1]
+
+        colVc <- unlist(read.table(eval(parse(text = paste0(tabC, "FilC"))),
+            check.names = FALSE,
+            nrow = 1,
+            sep = "\t"
+        ))[-1]
+
+        if (any(duplicated(rowVc))) {
+            stop("The following row name(s) is/are duplicated in the ",
+                tabNamC,
+                " table: '",
+                paste(rowVc[duplicated(rowVc)], collapse = "', '"), "'",
+                call. = FALSE
+            )
+        }
+
+        if (any(duplicated(colVc))) {
+            stop("The following column name(s) is/are duplicated in the ",
+                tabNamC,
+                " table: '",
+                paste(colVc[duplicated(colVc)], collapse = "', '"), "'",
+                call. = FALSE
+            )
+        }
+    }
+
+
+    ## reading tables
+
+    datMN <- t(as.matrix(read.table(datFilC,
+        check.names = FALSE,
+        header = TRUE,
+        row.names = 1,
+        sep = "\t"
+    )))
+
+    samDF <- read.table(samFilC,
+        check.names = FALSE,
+        header = TRUE,
+        row.names = 1,
+        sep = "\t"
+    )
+
+    varDF <- read.table(varFilC,
+        check.names = FALSE,
+        header = TRUE,
+        row.names = 1,
+        sep = "\t"
+    )
+
+
+    ## checking that dataMatrix is numeric and that the sample and variable numbers are coherent
+
+    if (mode(datMN) != "numeric") {
+        stop("The dataMatrix is not of the 'numeric' type",
+            call. = FALSE
+        )
+    }
+
+    if (nrow(datMN) != nrow(samDF)) {
+        if (nrow(datMN) > nrow(samDF)) {
+            print(setdiff(rownames(datMN), rownames(samDF)))
+            stop("The sample names above from dataMatrix were not found in sampleMetadata",
+                call. = FALSE
+            )
+        } else {
+            print(setdiff(rownames(samDF), rownames(datMN)))
+            stop("The sample names above from sampleMetadata were not found in dataMatrix",
+                call. = FALSE
+            )
+        }
+    }
+
+    if (ncol(datMN) != nrow(varDF)) {
+        if (ncol(datMN) > nrow(varDF)) {
+            print(setdiff(colnames(datMN), rownames(varDF)))
+            stop("The variable names above from dataMatrix were not found in variableMetadata",
+                call. = FALSE
+            )
+        } else {
+            print(setdiff(rownames(varDF), colnames(datMN)))
+            stop("The variable names above from variableMetadata were not found in dataMatrix",
+                call. = FALSE
+            )
+        }
+    }
+
+
+    ## making sample and variable names (optional)
+
+    newL <- FALSE
+
+    if (makNamL) {
+        cat("\n\nMessage: Converting sample and variable names to the standard R format\n")
+
+        rownames(datMN) <- make.names(rownames(datMN), unique = TRUE)
+        colnames(datMN) <- make.names(colnames(datMN), unique = TRUE)
+        rownames(samDF) <- make.names(rownames(samDF), unique = TRUE)
+        rownames(varDF) <- make.names(rownames(varDF), unique = TRUE)
+
+        newL <- TRUE
+    }
+
+
+    ## checking sample and variable names
+
+    chkL <- TRUE
+
+    if (!identical(rownames(datMN), rownames(samDF))) {
+        if (identical(sort(rownames(datMN)), sort(rownames(samDF)))) {
+            cat("\n\nMessage: Re-ordering dataMatrix sample names to match sampleMetadata\n")
+            datMN <- datMN[rownames(samDF), , drop = FALSE]
+
+            stopifnot(identical(sort(rownames(datMN)), sort(rownames(samDF))))
+
+            newL <- TRUE
+        } else {
+            cat("\n\nStop: The sample names of dataMatrix and sampleMetadata do not match:\n")
+            print(cbind.data.frame(
+                indice = 1:nrow(datMN),
+                dataMatrix = rownames(datMN),
+                sampleMetadata = rownames(samDF)
+            )[rownames(datMN) != rownames(samDF), , drop = FALSE])
+            chkL <- FALSE
+        }
+    }
+
+    if (!identical(colnames(datMN), rownames(varDF))) {
+        if (identical(sort(colnames(datMN)), sort(rownames(varDF)))) {
+            cat("\n\nMessage: Re-ordering dataMatrix variable names to match variableMetadata\n")
+            datMN <- datMN[, rownames(varDF), drop = FALSE]
+
+            stopifnot(identical(sort(colnames(datMN)), sort(rownames(varDF))))
+
+            newL <- TRUE
+        } else {
+            cat("\n\nStop: The variable names of dataMatrix and variableMetadata do not match:\n")
+            print(cbind.data.frame(
+                indice = 1:ncol(datMN),
+                dataMatrix = colnames(datMN),
+                variableMetadata = rownames(varDF)
+            )[colnames(datMN) != rownames(varDF), , drop = FALSE])
+            chkL <- FALSE
+        }
+    }
+
+
+    options(stringsAsFactors = optStrAsFacL)
+
+    resLs <- list(
+        chkL = chkL,
+        newL = newL,
+        datMN = datMN,
+        samDF = samDF,
+        varDF = varDF
+    )
+
+    return(resLs)
+} ## end of checkAndReadF
+
+write_dataMatrix <- function(dataMatrix, path) {
+    datDF <- cbind.data.frame(
+        dataMatrix = colnames(dataMatrix),
+        as.data.frame(t(dataMatrix))
+    )
+    write.table(datDF,
+        file = path,
+        quote = FALSE,
+        row.names = FALSE,
+        sep = "\t"
+    )
+}
+
+## sampleMetadata & variableMetadata
+write_metadata <- function(sampleMetadata, path) {
+    samDF <- cbind.data.frame(
+        sampleMetadata = rownames(sampleMetadata),
+        sampleMetadata
+    )
+    write.table(samDF,
+        file = path,
+        quote = FALSE,
+        row.names = FALSE,
+        sep = "\t"
+    )
+}
diff --git a/tools/checkformat/static/images/checkFormat_workflowPositionImage.png b/tools/checkformat/static/images/checkFormat_workflowPositionImage.png
new file mode 100644
index 000000000..c4f42813b
Binary files /dev/null and b/tools/checkformat/static/images/checkFormat_workflowPositionImage.png differ
diff --git a/tools/checkformat/test-data/input-dataMatrix.tsv b/tools/checkformat/test-data/input-dataMatrix.tsv
new file mode 100644
index 000000000..0ffcd7bce
--- /dev/null
+++ b/tools/checkformat/test-data/input-dataMatrix.tsv
@@ -0,0 +1,4 @@
+dataMatrix	HU_017	HU_021	HU_027	HU_032	HU_041	HU_048	HU_049	HU_050	HU_052	HU_059	HU_060	HU_066	HU_072	HU_077	HU_090	HU_109	HU_110	HU_125	HU_126	HU_131	HU_134	HU_149	HU_150	HU_173	HU_179	HU_180	HU_182	HU_202	HU_204	HU_209
+HMDB01032	2569204.924	6222035.774	17070707.99	1258838.243	13039543.08	1909391.77	3495.093864	2293521.909	128503.2751	81872.52764	8103557.566	149574887	1544036.41	7103429.539	14138796.5	4970265.58	263054.7306	1671332.3	88433.1945	23602331.29	18648126.52	1554657.988	34152.36464	209372.7128	33187733.37	202438.5916	13581070.09	354170.8107	9120781.49	43419175.41
+HMDB03072	3628416.303	65626.98344	112170.1189	3261804.344	42228.27877	343254.2013	1958217.693	11983270.04	5932111.416	5511385.834	9154521.478	2632133.212	9500411.146	6551644.517	7204319.809	1273412.048	3260583.816	8932005.535	8340827.526	9256460.692	11217839.17	5919262.814	11790077.07	9567977.808	73717.58117	9991787.291	4208098.147	623970.6499	10904221.26	2171793.936
+HMDB00792	429568.6094	3887629.505	1330692.117	1367446.73	844197.4475	2948090.719	1614157.906	3740009.194	3292251.665	2310688.795	4404239.59	3043289.128	825736.4672	2523241.917	6030501.026	474901.6041	2885792.426	2955990.64	1917716.343	1767962.677	5926203.404	1639065.695	346810.7636	1054776.223	2390258.275	1831346.373	1026696.369	7079792.5	4368341.014	3495986.873
diff --git a/tools/checkformat/test-data/input-sampleMetadata.tsv b/tools/checkformat/test-data/input-sampleMetadata.tsv
new file mode 100644
index 000000000..d0c01a6f2
--- /dev/null
+++ b/tools/checkformat/test-data/input-sampleMetadata.tsv
@@ -0,0 +1,31 @@
+sampleMetadata	age	ageGrp
+HU_017	41	experienced
+HU_021	34	junior
+HU_027	37	experienced
+HU_032	38	experienced
+HU_041	28	junior
+HU_048	39	experienced
+HU_049	50	senior
+HU_050	30	junior
+HU_052	51	senior
+HU_059	81	senior
+HU_060	55	senior
+HU_066	25	junior
+HU_072	47	experienced
+HU_077	27	junior
+HU_090	46	experienced
+HU_109	32	junior
+HU_110	50	senior
+HU_125	58	senior
+HU_126	45	experienced
+HU_131	42	experienced
+HU_134	48	experienced
+HU_149	35	experienced
+HU_150	49	experienced
+HU_173	55	senior
+HU_179	33	junior
+HU_180	53	senior
+HU_182	43	experienced
+HU_202	42	experienced
+HU_204	31	junior
+HU_209	17.5	junior
diff --git a/tools/checkformat/test-data/input-variableMetadata.tsv b/tools/checkformat/test-data/input-variableMetadata.tsv
new file mode 100644
index 000000000..42d0ad93f
--- /dev/null
+++ b/tools/checkformat/test-data/input-variableMetadata.tsv
@@ -0,0 +1,4 @@
+variableMetadata	name
+HMDB01032	Dehydroepiandrosterone sulfate
+HMDB03072	Quinic acid
+HMDB00792	Sebacic acid
diff --git a/tools/checkformat/test-data/output-dataMatrix.tsv b/tools/checkformat/test-data/output-dataMatrix.tsv
new file mode 100644
index 000000000..d07105a32
--- /dev/null
+++ b/tools/checkformat/test-data/output-dataMatrix.tsv
@@ -0,0 +1,4 @@
+dataMatrix	X17	HU_021	HU_027	HU_032	HU_041	HU_048	HU_049	HU_050	HU_052	HU_059	HU_060	HU_066	HU_072	HU_077	HU_090	HU_109	HU_110	HU_125	HU_126	HU_131	HU_134	HU_149	HU_150	HU_173	HU_179	HU_180	HU_182	HU_202	HU_204	HU_209
+HMDB01032	2569204.924	6222035.774	17070707.99	1258838.243	13039543.08	1909391.77	3495.093864	2293521.909	128503.2751	81872.52764	8103557.566	149574887	1544036.41	7103429.539	14138796.5	4970265.58	263054.7306	1671332.3	88433.1945	23602331.29	18648126.52	1554657.988	34152.36464	209372.7128	33187733.37	202438.5916	13581070.09	354170.8107	9120781.49	43419175.41
+HMDB03072	3628416.303	65626.98344	112170.1189	3261804.344	42228.27877	343254.2013	1958217.693	11983270.04	5932111.416	5511385.834	9154521.478	2632133.212	9500411.146	6551644.517	7204319.809	1273412.048	3260583.816	8932005.535	8340827.526	9256460.692	11217839.17	5919262.814	11790077.07	9567977.808	73717.58117	9991787.291	4208098.147	623970.6499	10904221.26	2171793.936
+HMDB00792	429568.6094	3887629.505	1330692.117	1367446.73	844197.4475	2948090.719	1614157.906	3740009.194	3292251.665	2310688.795	4404239.59	3043289.128	825736.4672	2523241.917	6030501.026	474901.6041	2885792.426	2955990.64	1917716.343	1767962.677	5926203.404	1639065.695	346810.7636	1054776.223	2390258.275	1831346.373	1026696.369	7079792.5	4368341.014	3495986.873
diff --git a/tools/checkformat/test-data/output-information.txt b/tools/checkformat/test-data/output-information.txt
new file mode 100644
index 000000000..2cd78cbad
--- /dev/null
+++ b/tools/checkformat/test-data/output-information.txt
@@ -0,0 +1,26 @@
+
+Start of the 'Check Format' Galaxy module call: Thu 26 Oct 2017 10:27:44 AM
+
+Table formats are OK; enjoy your analyses!
+
+End of the 'Check Format' Galaxy module call: Thu 26 Oct 2017 10:27:44 AM
+
+
+
+============================================================================
+Additional information about the call:
+
+1) Parameters:
+                    value                                   
+dataMatrix_in       "/tmp/tmpolhAXS/files/000/dataset_1.dat"
+sampleMetadata_in   "/tmp/tmpolhAXS/files/000/dataset_2.dat"
+variableMetadata_in "/tmp/tmpolhAXS/files/000/dataset_3.dat"
+information         "/tmp/tmpolhAXS/files/000/dataset_4.dat"
+
+2) Session Info:
+R version 3.3.2 (2016-10-31) 
+Main packages:
+batch 1.1.4 	
+Other loaded packages:
+
+============================================================================